This research aims to determine if the postoperative function of a total knee replacement recipient can be modeled based on anthropomorphic data and details of the surgical procedure. We decided to carry out testing on models with two postoperative scoring systems as the response variable. The first score is the “Surgeon’s Score” which measures more objective postoperative metrics about the condition of the replaced knee following surgery. These metrics include: how straight or how flexed the patient can make thier knee, how well aligned the knee appears when inspecting from a frontal perspective and how much laxity or separation can be achieved by placing the lower leg under tension. Finally, the patient is asked about the overall pain they experience with the knee. The resulting score is a value between 0-100 with 80-100 being an excellent result.
The second score we model is the “Patient’s Score” which is generated by three questions: how far are they able to walk, how well can they navigate stairs and do they require any walking aids (crutches, cane, etc).
We hope to create a model that can predict each of the scores based on a variety of categorical and numeric predictors.
This data has been collected from a Southern California Hospital in collaboration with the Shiley Center for Orthopedic Research. The data is used for both clinical research and postoperative monitoring of implant survivorship. All patient specific information has been removed from the data so it adheres to the Health Insurance Portability and Accountability Act (HIPAA).
We hope to determine the impact a particular surgeon or the type of implants used has on the patient’s outcome after surgery. We are also interested in exploring the potential relationship between anthropomorphic factors and the patient’s postoperative satisfaction. Finally, we would like to understand if the considerable expense of computer navigation in knee replacement leads to better postoperative scores. Nevertheless, we keep our option opened to investigate other aspects that were not ‘visibile’ or never thought about it but might reveal themselfs as we move on with the project.
Here we may consider KneeScore_Surgeon or KneeScore_Patient as response and Age, Gendar, Weight, Height, BMI, Race, Side, Manufacturer as predictors. Gendar, Race, Side and Manufacturer are some of the categorical predictors and Age, Height, Weight and BMI are numerical predictors.
knee = read.csv('knees.csv')
knee$Surgeon = as.factor(knee$Surgeon)
knee$Year = as.factor(knee$Year)
#Function to plot various plots as QQPlot, Fitted vs Residual Plot.
plots = function(model) {
par(mfcol=c(2,2))
qqnorm(resid(model), col = red, pch = 16)
qqline(resid(model), col = lightblue, lwd = 2)
plot(fitted(model), resid(model), xlab = 'Fitted Values', ylab = 'Residuals', main = 'Fitted vs. Residuals Plot', col = purple, pch = 16)
abline(h = 0, col = green, lwd = 2)
hist(resid(model), col = blue, main = 'Histogram of Residuals', xlab = 'Residuals')
}
#Function to calculate various statistics which we use to evaluate the model
evaluate = function(model){
# Run each of the tests
lambda = 1.000001 # this is a hack so the function will return a CrossValidation score - HatValues of 1.0 are causing a division by zero error.
shapiroTest = shapiro.test(resid(model))
bpTest = bptest(model)
rSquared = summary(model)$r.squared
adjRSquared = summary(model)$adj.r.squared
loocv = sqrt(mean((resid(model) / (lambda - hatvalues(model))) ^ 2))
large_hat = sum(hatvalues(model) > 2 * mean(hatvalues(model)))
large_resid = sum(rstandard(model)[abs(rstandard(model)) > 2]) / (length(rstandard(model) + lambda))
# Collect tests in dataframe
values = data.frame(Result = c(prettyNum(shapiroTest$p.value), prettyNum(bpTest$p.value), prettyNum(rSquared), prettyNum(adjRSquared),prettyNum(loocv), prettyNum(large_hat)))
rowNames = data.frame(Test = c('Shapiro Wilk pvalue', 'Breusch-Pagan pvalue', 'R Squared', 'Adj R Squared', 'Cross Validation', 'Large Hat Values'))
summary_output = cbind(rowNames, values)
show(summary_output)
plots(model)
}
# find and remove all influential values and return the resulting dataframe
removeInfluential = function(model, data){
large_lev_index = which(hatvalues(model) > 2 * mean(hatvalues(model)))
cooks = which(cooks.distance(model) > 4 / length(cooks.distance(model)))
rStandard = abs(rstandard(model))
rStandardIndex = which(rStandard > 2)
index_ = intersect(intersect(large_lev_index, cooks), rStandardIndex)
newData = data[-index_ , ]
return(newData)
}
# identify all influential data points
IdentifyInfluential = function(model, data){
large_lev_index = which(hatvalues(model) > 2 * mean(hatvalues(model)))
cooks = which(cooks.distance(model) > 4 / length(cooks.distance(model)))
rStandard = abs(rstandard(model))
rStandardIndex = which(rStandard > 2)
index_ = intersect(intersect(large_lev_index, cooks), rStandardIndex)
return(index_)
}
# find large hat values, subtract them from the dataframe and return the dataframe
removeLargeHatValues = function(model, data){
largeHat = which(hatvalues(model) > 2 * mean(hatvalues(model)))
newData = data[-largeHat, ]
return(newData)
}
# calculate the prediction accuracy with a margin (i.e. if the margin is set to 2, then a predicted value of 35.5 will return true if the actual value is 33.5-37.5)
prediction_accuracy = function(model, data, margin) {
upper = data + margin
lower = data - margin
prediction = predict(model, newdata = data)
return(sum(prediction < upper & lower < prediction)) / length(prediction)
}
rmse = function(actual, predicted) { sqrt(mean((actual - predicted) ^ 2))}
Begin by fitting a full additive model as a baseline and evaluating.
surgeon_full_additive_model = lm(KneeScore_Surgeon ~ ., data = knee)
evaluate(surgeon_full_additive_model)
## Test Result
## 1 Shapiro Wilk pvalue 2.080142e-08
## 2 Breusch-Pagan pvalue 0.9192514
## 3 R Squared 0.2718411
## 4 Adj R Squared 0.2130606
## 5 Cross Validation 14.4126
## 6 Large Hat Values 177
The baseline model has many large hat values. Let’s try to understand why.
largeHat = which(hatvalues(surgeon_full_additive_model) > (2 * mean(hatvalues(surgeon_full_additive_model))))
unique(largeHat)
## [1] 7 9 10 17 19 28 30 40 52 74 78 80 87 91
## [15] 110 118 121 123 125 149 154 161 198 233 234 235 236 237
## [29] 238 240 243 244 257 258 280 302 343 347 352 354 369 371
## [43] 372 397 400 404 427 446 461 473 482 505 527 529 530 531
## [57] 532 533 534 535 544 547 552 554 559 573 638 679 681 689
## [71] 700 703 763 785 818 844 849 876 881 883 885 888 891 933
## [85] 952 976 979 989 996 1030 1032 1047 1055 1057 1060 1063 1064 1065
## [99] 1066 1067 1077 1093 1096 1099 1104 1107 1117 1159 1161 1178 1182 1202
## [113] 1213 1220 1241 1245 1246 1252 1257 1273 1284 1352 1370 1374 1376 1379
## [127] 1385 1386 1392 1406 1415 1431 1450 1466 1467 1488 1500 1502 1503 1515
## [141] 1517 1521 1522 1523 1540 1541 1544 1554 1568 1572 1587 1601 1617 1686
## [155] 1689 1692 1694 1700 1746 1762 1771 1773 1774 1775 1778 1781 1783 1784
## [169] 1785 1863 1864 1865 1914 1919 1927 1938 1939
print(knee[689, ])
## Surgeon Year Age Gender Weight Height BMI Diagnosis
## 689 4 2012 68 Female 162 63 28.72 Osteoarthritis
## Race Side KneeScore_Surgeon KneeScore_Patient GPS
## 689 Mid-East Arabian Right 50 50 No
## Manufacturer FemoralComponentModel FemoralComponentSize
## 689 Stryker Triathlon 4
## FemoralComponentType TibialTrayModel TibialTraySize TibialInsertModel
## 689 cruciate retaining Triathlon 4 Triathlon
## TibialInsertWidth TibialInsertType PatellaModel
## 689 11 high flex Triathlon Asymmetric Patella
## PatellaDiameter
## 689 39
print(knee[1927, ])
## Surgeon Year Age Gender Weight Height BMI Diagnosis Race
## 1927 1 2015 62 Male 200 68 30.44 Osteoarthritis White
## Side KneeScore_Surgeon KneeScore_Patient GPS Manufacturer
## 1927 Bilateral 42 50 No Smith & Nephew
## FemoralComponentModel FemoralComponentSize FemoralComponentType
## 1927 Legion 8+ cruciate retaining
## TibialTrayModel TibialTraySize TibialInsertModel TibialInsertWidth
## 1927 Genesis II 7 Legion CR XLPE 13
## TibialInsertType PatellaModel PatellaDiameter
## 1927 high flex Genesis II 38
After inspection of the rows that represent the large hat values it seems that there are a preponderence of values that are either errant entries or valid, but rare entries. For example, the Race predictor has only two entries for Mid-East Arabian and the FemoralComponentSize entry of ‘8+’ is errant. First we will attempt to remove the predictors that seem to be prone to errant or rare values and later we will remove the high leverage values directly.
We attempted several model iterations with tranformations of both the response and predictors as well as large all two-way interaction models none of which proved helpful in predicting the response. The models with many interactions took both substatantial time and computing resources to fit and were suspect of overfitting. We pick up here with model eight which was the first of the promising models. The interested reader can find earlier attempted model in the appendix.
surgeon_model_eight = lm(KneeScore_Surgeon ~ . - Diagnosis - Race - TibialInsertType - FemoralComponentModel - PatellaModel - TibialTrayModel - TibialTraySize - FemoralComponentType, data = knee)
evaluate(surgeon_model_eight)
## Test Result
## 1 Shapiro Wilk pvalue 3.989833e-07
## 2 Breusch-Pagan pvalue 0.1270351
## 3 R Squared 0.2374036
## 4 Adj R Squared 0.2084443
## 5 Cross Validation 14.34844
## 6 Large Hat Values 126
anova(surgeon_model_eight, surgeon_full_additive_model)
## Analysis of Variance Table
##
## Model 1: KneeScore_Surgeon ~ (Surgeon + Year + Age + Gender + Weight +
## Height + BMI + Diagnosis + Race + Side + KneeScore_Patient +
## GPS + Manufacturer + FemoralComponentModel + FemoralComponentSize +
## FemoralComponentType + TibialTrayModel + TibialTraySize +
## TibialInsertModel + TibialInsertWidth + TibialInsertType +
## PatellaModel + PatellaDiameter) - Diagnosis - Race - TibialInsertType -
## FemoralComponentModel - PatellaModel - TibialTrayModel -
## TibialTraySize - FemoralComponentType
## Model 2: KneeScore_Surgeon ~ Surgeon + Year + Age + Gender + Weight +
## Height + BMI + Diagnosis + Race + Side + KneeScore_Patient +
## GPS + Manufacturer + FemoralComponentModel + FemoralComponentSize +
## FemoralComponentType + TibialTrayModel + TibialTraySize +
## TibialInsertModel + TibialInsertWidth + TibialInsertType +
## PatellaModel + PatellaDiameter
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 1896 379610
## 2 1821 362468 75 17142 1.1483 0.1845
While removing the predictors doesn’t yeild a definatively better model at a reasonable \(\alpha\), it does increase Adjusted \(R^2\) and slightly improves the cross validation score.
Utilize a Bayesian Information Criterion approach and evaluate the selected model.
n = length(resid(surgeon_full_additive_model))
surgeon_model_back_bic = step(surgeon_full_additive_model, direction = "backward", k = log(n), trace = 0)
evaluate(surgeon_model_back_bic)
## Test Result
## 1 Shapiro Wilk pvalue 1.169168e-05
## 2 Breusch-Pagan pvalue 0.0001309477
## 3 R Squared 0.1869122
## 4 Adj R Squared 0.1852562
## 5 Cross Validation 14.37628
## 6 Large Hat Values 87
anova(surgeon_model_back_bic, surgeon_full_additive_model)
## Analysis of Variance Table
##
## Model 1: KneeScore_Surgeon ~ Age + Side + KneeScore_Patient
## Model 2: KneeScore_Surgeon ~ Surgeon + Year + Age + Gender + Weight +
## Height + BMI + Diagnosis + Race + Side + KneeScore_Patient +
## GPS + Manufacturer + FemoralComponentModel + FemoralComponentSize +
## FemoralComponentType + TibialTrayModel + TibialTraySize +
## TibialInsertModel + TibialInsertWidth + TibialInsertType +
## PatellaModel + PatellaDiameter
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 1964 404744
## 2 1821 362468 143 42276 1.4853 0.000288 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
The resulting BIC model scores marginally better in Cross Validation though the anova results clearly prefer the full additive model.
Next, we will evaluate the RMSE of the best performing models thus far.
options(warn=-1)
sample_idx = sample(1:nrow(knee), 1500)
train_data = knee[sample_idx, ]
test_data = knee[-sample_idx, ]
full_test = rmse(test_data$KneeScore_Surgeon, predict(surgeon_full_additive_model, test_data))
full_train = rmse(train_data$KneeScore_Surgeon, predict(surgeon_full_additive_model, train_data))
test_mod_8 = rmse(test_data$KneeScore_Surgeon, predict(surgeon_model_eight, test_data))
train_mod_8 = rmse(train_data$KneeScore_Surgeon, predict(surgeon_model_eight, train_data))
bic_test = rmse(test_data$KneeScore_Surgeon, predict(surgeon_model_back_bic, test_data))
bic_train = rmse(train_data$KneeScore_Surgeon, predict(surgeon_model_back_bic, train_data))
| Model | Train RMSE | Test RMSE |
|---|---|---|
Model All+ |
13.6920687 | 13.1627856 |
Model 8 |
13.9816352 | 13.5713295 |
Model BIC |
14.40996 | 14.1023973 |
The full model delivers the best RMSE as well as
Perhaps removing some influential data points will assist in creating a better model. Next we remove influential points that satisfy the criteria for Large Leverage, Large Cook's Distance and Large RStandard values.
new_dataframe = removeInfluential(surgeon_model_eight, knee)
surgeon_model_nine = lm(KneeScore_Surgeon ~ . - Diagnosis - Race - TibialInsertType - FemoralComponentModel - PatellaModel - TibialTrayModel - TibialTraySize - FemoralComponentType, data = new_dataframe)
evaluate(surgeon_model_nine)
## Test Result
## 1 Shapiro Wilk pvalue 6.718107e-07
## 2 Breusch-Pagan pvalue 0.2390135
## 3 R Squared 0.241005
## 4 Adj R Squared 0.2124774
## 5 Cross Validation 14.17558
## 6 Large Hat Values 119
This does seem to be of moderate benefit in relation to Adjusted \(R^2\) and Cross Validation.
We will evaluate the same model one again after removing the identified large hat values.
remove_hat_dataframe = removeLargeHatValues(surgeon_model_nine, new_dataframe)
surgeon_model_ten = lm(KneeScore_Surgeon ~ . - Diagnosis - Race - TibialInsertType - FemoralComponentModel - PatellaModel - TibialTrayModel - TibialTraySize - FemoralComponentType, data = remove_hat_dataframe)
evaluate(surgeon_model_ten)
## Test Result
## 1 Shapiro Wilk pvalue 3.604033e-06
## 2 Breusch-Pagan pvalue 0.08198251
## 3 R Squared 0.2187277
## 4 Adj R Squared 0.2013757
## 5 Cross Validation 14.32124
## 6 Large Hat Values 93
Removing the large hat values decreased the Cross Validation score. Perhaps we can find a better model by running BIC on the modified dataframe.
n = length(resid(surgeon_model_ten))
surgeon_model_10_bic = step(surgeon_model_ten, direction = "backward", k = log(n), trace = 0)
evaluate(surgeon_model_10_bic)
## Test Result
## 1 Shapiro Wilk pvalue 0.0001065612
## 2 Breusch-Pagan pvalue 8.666681e-05
## 3 R Squared 0.1862472
## 4 Adj R Squared 0.1844753
## 5 Cross Validation 14.33378
## 6 Large Hat Values 79
Despite the reduction in leveraged values the selected model is no better than preceeding models.
sample_idx_two = sample(1:nrow(remove_hat_dataframe), 1300)
train_data_two = remove_hat_dataframe[sample_idx_two, ]
test_data_two = remove_hat_dataframe[-sample_idx_two, ]
test_mod_10 = rmse(test_data_two$KneeScore_Surgeon, predict(surgeon_model_ten, train_data_two))
train_mod_10 = rmse(train_data_two$KneeScore_Surgeon, predict(surgeon_model_ten, train_data_two))
test_10_bic = rmse(test_data_two$KneeScore_Surgeon, predict(surgeon_model_10_bic, train_data_two))
train_10_bic = rmse(train_data_two$KneeScore_Surgeon, predict(surgeon_model_10_bic, train_data_two))
| Model | Train RMSE | Test RMSE |
|---|---|---|
Model 10 |
14.0424519 | 17.1835625 |
Model 10 BIC |
14.313086 | 17.0115541 |
Removing the large hat values has had the opposite intended effect of decreasing the RMSE values.
Begin by fitting a full additive model as a baseline and evaluating.
pat_full_additive_model = lm(KneeScore_Patient ~ ., data = knee)
evaluate(pat_full_additive_model)
## Test Result
## 1 Shapiro Wilk pvalue 1.941649e-14
## 2 Breusch-Pagan pvalue 0.9539336
## 3 R Squared 0.3161338
## 4 Adj R Squared 0.2609288
## 5 Cross Validation 17.07365
## 6 Large Hat Values 178
The baseline model has many large leverage values, which, upon inspection may be coming from several of the implant fields. Perhaps removing the suspect implant predictors will help improve the model.
pat_model_eight = lm(KneeScore_Patient ~ . - Diagnosis - Race - TibialInsertType - FemoralComponentModel - PatellaModel - TibialTrayModel - TibialTraySize - FemoralComponentType, data = knee)
evaluate(pat_model_eight)
## Test Result
## 1 Shapiro Wilk pvalue 1.115521e-14
## 2 Breusch-Pagan pvalue 0.00453633
## 3 R Squared 0.2810507
## 4 Adj R Squared 0.2537489
## 5 Cross Validation 16.88212
## 6 Large Hat Values 126
anova(pat_model_eight, pat_full_additive_model)
## Analysis of Variance Table
##
## Model 1: KneeScore_Patient ~ (Surgeon + Year + Age + Gender + Weight +
## Height + BMI + Diagnosis + Race + Side + KneeScore_Surgeon +
## GPS + Manufacturer + FemoralComponentModel + FemoralComponentSize +
## FemoralComponentType + TibialTrayModel + TibialTraySize +
## TibialInsertModel + TibialInsertWidth + TibialInsertType +
## PatellaModel + PatellaDiameter) - Diagnosis - Race - TibialInsertType -
## FemoralComponentModel - PatellaModel - TibialTrayModel -
## TibialTraySize - FemoralComponentType
## Model 2: KneeScore_Patient ~ Surgeon + Year + Age + Gender + Weight +
## Height + BMI + Diagnosis + Race + Side + KneeScore_Surgeon +
## GPS + Manufacturer + FemoralComponentModel + FemoralComponentSize +
## FemoralComponentType + TibialTrayModel + TibialTraySize +
## TibialInsertModel + TibialInsertWidth + TibialInsertType +
## PatellaModel + PatellaDiameter
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 1896 530943
## 2 1821 505034 75 25909 1.2456 0.07874 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
While removing the predictors doesn’t yeild a definatively better model at a reasonable \(\alpha\), it does increase Adjusted \(R^2\) and slightly improves the cross validation score.
Utilize a Bayesian Information Criterion approach and evaluate the selected model.
n = length(resid(pat_full_additive_model))
pat_model_back_bic = step(pat_full_additive_model, direction = "backward", k = log(n), trace = 0)
evaluate(pat_model_back_bic)
## Test Result
## 1 Shapiro Wilk pvalue 1.934109e-15
## 2 Breusch-Pagan pvalue 7.743929e-07
## 3 R Squared 0.2423439
## 4 Adj R Squared 0.2404141
## 5 Cross Validation 16.91176
## 6 Large Hat Values 112
anova(pat_model_back_bic, pat_full_additive_model)
## Analysis of Variance Table
##
## Model 1: KneeScore_Patient ~ Age + Gender + Weight + Height + KneeScore_Surgeon
## Model 2: KneeScore_Patient ~ Surgeon + Year + Age + Gender + Weight +
## Height + BMI + Diagnosis + Race + Side + KneeScore_Surgeon +
## GPS + Manufacturer + FemoralComponentModel + FemoralComponentSize +
## FemoralComponentType + TibialTrayModel + TibialTraySize +
## TibialInsertModel + TibialInsertWidth + TibialInsertType +
## PatellaModel + PatellaDiameter
## Res.Df RSS Df Sum of Sq F Pr(>F)
## 1 1963 559528
## 2 1821 505034 142 54494 1.3837 0.002592 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
The resulting BIC model scores marginally better in Cross Validation though the anova results clearly prefer the full additive model.
Next, we will evaluate the RMSE of the best performing models thus far.
options(warn=-1)
sample_idx = sample(1:nrow(knee), 1500)
train_data = knee[sample_idx, ]
test_data = knee[-sample_idx, ]
rmse = function(actual, predicted) { sqrt(mean((actual - predicted) ^ 2))}
pat_full_test = rmse(test_data$KneeScore_Patient, predict(pat_full_additive_model, test_data))
pat_full_train = rmse(train_data$KneeScore_Patient, predict(pat_full_additive_model, train_data))
pat_test_mod_8 = rmse(test_data$KneeScore_Patient, predict(pat_model_eight, test_data))
pat_train_mod_8 = rmse(train_data$KneeScore_Patient, predict(pat_model_eight, train_data))
pat_bic_test = rmse(test_data$KneeScore_Patient, predict(pat_model_back_bic, test_data))
pat_bic_train = rmse(train_data$KneeScore_Patient, predict(pat_model_back_bic, train_data))
| Model | Train RMSE | Test RMSE |
|---|---|---|
Model All+ |
13.6920687 | 13.1627856 |
Model 8 |
13.9816352 | 13.5713295 |
Model BIC |
14.40996 | 14.1023973 |
The additive model with all predictors has the best RMSE values.
Perhaps removing some influential data points will assist in creating a better model. Next we remove influential points that satisfy the criteria for Large Leverage, Large Cook's Distance and Large RStandard values.
new_dataframe = removeInfluential(pat_model_eight, knee)
pat_model_nine = lm(KneeScore_Patient ~ . - Diagnosis - Race - TibialInsertType - FemoralComponentModel - PatellaModel - TibialTrayModel - TibialTraySize - FemoralComponentType, data = new_dataframe)
evaluate(pat_model_nine)
## Test Result
## 1 Shapiro Wilk pvalue 2.138818e-14
## 2 Breusch-Pagan pvalue 0.006017515
## 3 R Squared 0.2818728
## 4 Adj R Squared 0.25453
## 5 Cross Validation 16.75786
## 6 Large Hat Values 122
This does seem to be of moderate benefit in relation to Adjusted \(R^2\) and Cross Validation.
We will evaluate the same model one again after removing the identified large hat values.
remove_hat_dataframe = removeLargeHatValues(pat_model_nine, new_dataframe)
pat_model_ten = lm(KneeScore_Patient ~ . - Diagnosis - Race - TibialInsertType - FemoralComponentModel - PatellaModel - TibialTrayModel - TibialTraySize - FemoralComponentType, data = remove_hat_dataframe)
evaluate(pat_model_ten)
## Test Result
## 1 Shapiro Wilk pvalue 1.502033e-13
## 2 Breusch-Pagan pvalue 0.0001416128
## 3 R Squared 0.2753799
## 4 Adj R Squared 0.2592862
## 5 Cross Validation 16.92845
## 6 Large Hat Values 94
Removing the large hat values decreased the Cross Validation score. Perhaps we can find a better model by running BIC on the modified dataframe.
n = length(resid(pat_model_ten))
pat_model_10_bic = step(pat_model_ten, direction = "backward", k = log(n), trace = 0)
evaluate(pat_model_10_bic)
## Test Result
## 1 Shapiro Wilk pvalue 1.298166e-14
## 2 Breusch-Pagan pvalue 1.347535e-06
## 3 R Squared 0.2491407
## 4 Adj R Squared 0.2470959
## 5 Cross Validation 16.91151
## 6 Large Hat Values 101
Despite the reduction in leveraged values the selected model is no better than preceeding models.
sample_idx_two = sample(1:nrow(remove_hat_dataframe), 1300)
train_data_two = remove_hat_dataframe[sample_idx_two, ]
test_data_two = remove_hat_dataframe[-sample_idx_two, ]
test_mod_10 = rmse(test_data_two$KneeScore_Patient, predict(pat_model_ten, train_data_two))
train_mod_10 = rmse(train_data_two$KneeScore_Patient, predict(pat_model_ten, train_data_two))
test_10_bic = rmse(test_data_two$KneeScore_Patient, predict(pat_model_10_bic, train_data_two))
train_10_bic = rmse(train_data_two$KneeScore_Patient, predict(pat_model_10_bic, train_data_two))
| Model | Train RMSE | Test RMSE |
|---|---|---|
Model 10 |
16.6282358 | 21.7155956 |
Model 10 BIC |
16.8517414 | 21.4036662 |
Interestingly the models fit on the dataset without leverages fares worse on test RMSE.
pat_model = lm(KneeScore_Patient ~. , data = knee)
pat_model_back_aic = step(pat_model, direction = "backward", trace = 0)
pat_model_for_aic = step(pat_model, direction = "forward", trace = 0)
pat_model_both_aic = step(pat_model, direction = "both", trace = 0)
n = length(resid(pat_model))
pat_model_back_bic = step(pat_model, direction = "backward", k = log(n), trace = 0)
pat_model_for_bic = step(pat_model, direction = "forward", k = log(n), trace = 0)
pat_model_both_bic = step(pat_model, direction = "both", k = log(n), trace = 0)
evaluate(pat_model)
## Test Result
## 1 Shapiro Wilk pvalue 1.941649e-14
## 2 Breusch-Pagan pvalue 0.9539336
## 3 R Squared 0.3161338
## 4 Adj R Squared 0.2609288
## 5 Cross Validation 17.07365
## 6 Large Hat Values 178
evaluate(pat_model_back_aic)
## Test Result
## 1 Shapiro Wilk pvalue 1.123084e-14
## 2 Breusch-Pagan pvalue 2.237347e-05
## 3 R Squared 0.2562632
## 4 Adj R Squared 0.2490128
## 5 Cross Validation 16.85518
## 6 Large Hat Values 147
evaluate(pat_model_for_aic)
## Test Result
## 1 Shapiro Wilk pvalue 1.941649e-14
## 2 Breusch-Pagan pvalue 0.9539336
## 3 R Squared 0.3161338
## 4 Adj R Squared 0.2609288
## 5 Cross Validation 17.07365
## 6 Large Hat Values 178
evaluate(pat_model_both_aic)
## Test Result
## 1 Shapiro Wilk pvalue 1.123084e-14
## 2 Breusch-Pagan pvalue 2.237347e-05
## 3 R Squared 0.2562632
## 4 Adj R Squared 0.2490128
## 5 Cross Validation 16.85518
## 6 Large Hat Values 147
## Adj.R.Squared: 0.24 - CrossValidation: 16.9
evaluate(pat_model_back_bic)
## Test Result
## 1 Shapiro Wilk pvalue 1.934109e-15
## 2 Breusch-Pagan pvalue 7.743929e-07
## 3 R Squared 0.2423439
## 4 Adj R Squared 0.2404141
## 5 Cross Validation 16.91176
## 6 Large Hat Values 112
evaluate(pat_model_for_bic)
## Test Result
## 1 Shapiro Wilk pvalue 1.941649e-14
## 2 Breusch-Pagan pvalue 0.9539336
## 3 R Squared 0.3161338
## 4 Adj R Squared 0.2609288
## 5 Cross Validation 17.07365
## 6 Large Hat Values 178
evaluate(pat_model_both_bic)
## Test Result
## 1 Shapiro Wilk pvalue 1.934109e-15
## 2 Breusch-Pagan pvalue 7.743929e-07
## 3 R Squared 0.2423439
## 4 Adj R Squared 0.2404141
## 5 Cross Validation 16.91176
## 6 Large Hat Values 112
## Remove large leverages
new_data = removeInfluential(pat_model, knee)
pat_model_without_large_leverages = lm(KneeScore_Patient ~ ., data = new_data)
evaluate(pat_model_without_large_leverages)
## Test Result
## 1 Shapiro Wilk pvalue 1.061121e-14
## 2 Breusch-Pagan pvalue 0.9760654
## 3 R Squared 0.3171425
## 4 Adj R Squared 0.2622432
## 5 Cross Validation 16.88624
## 6 Large Hat Values 174
Removing the records with large hat values and refitting simply introduces more large hat values. What is unique about these rows of data?
which(hatvalues(pat_model) == 1.0)
## 17 19 74 80 240 244 258 354 400 533 638 703 763 844 876
## 17 19 74 80 240 244 258 354 400 533 638 703 763 844 876
## 881 891 1093 1096 1245 1374 1406 1544 1554 1686 1775 1778 1781 1919 1927
## 881 891 1093 1096 1245 1374 1406 1544 1554 1686 1775 1778 1781 1919 1927
## 1938
## 1938
print(knee[17,])
## Surgeon Year Age Gender Weight Height BMI Diagnosis Race Side
## 17 3 2010 68 Female 148 64 25.43 Osteoarthritis White Left
## KneeScore_Surgeon KneeScore_Patient GPS Manufacturer
## 17 48 50 No DePuy (J&J)
## FemoralComponentModel FemoralComponentSize FemoralComponentType
## 17 Nonporous 2 cruciate retaining
## TibialTrayModel TibialTraySize TibialInsertModel TibialInsertWidth
## 17 PFC Sigma 2.5 PFC Sigma 8
## TibialInsertType PatellaModel PatellaDiameter
## 17 curved 3-Post Round Dome 32
print(knee[240,])
## Surgeon Year Age Gender Weight Height BMI Diagnosis Race
## 240 3 2010 66 Female 130 68 19.78 Osteoarthritis White
## Side KneeScore_Surgeon KneeScore_Patient GPS Manufacturer
## 240 Bilateral 60 80 No Zimmer
## FemoralComponentModel FemoralComponentSize FemoralComponentType
## 240 Zimmer Precoat E - cruciate retaining
## TibialTrayModel TibialTraySize TibialInsertModel TibialInsertWidth
## 240 Nexgen 4 Nexgen 10
## TibialInsertType PatellaModel PatellaDiameter
## 240 standard NexGen 32
print(knee[638,])
## Surgeon Year Age Gender Weight Height BMI Diagnosis Race Side
## 638 3 2012 67 Female 167 62 30.57 Osteoarthritis White Right
## KneeScore_Surgeon KneeScore_Patient GPS Manufacturer
## 638 55 55 Yes DePuy (J&J)
## FemoralComponentModel FemoralComponentSize FemoralComponentType
## 638 Sigma 4N cruciate retaining
## TibialTrayModel TibialTraySize TibialInsertModel TibialInsertWidth
## 638 PFC Sigma 3 PFC Sigma 8
## TibialInsertType PatellaModel PatellaDiameter
## 638 high flex,Fixed bearing Triathlon Asymmetric Patella 35
print(knee[1093,])
## Surgeon Year Age Gender Weight Height BMI Diagnosis Race
## 1093 3 2013 83 Female 130 63 23.05 Osteoarthritis White
## Side KneeScore_Surgeon KneeScore_Patient GPS Manufacturer
## 1093 Right 66 50 No DePuy (J&J)
## FemoralComponentModel FemoralComponentSize FemoralComponentType
## 1093 Sigma 3 posterior stabilized
## TibialTrayModel TibialTraySize TibialInsertModel TibialInsertWidth
## 1093 PFC Sigma 2.5 PFC Sigma 8
## TibialInsertType PatellaModel PatellaDiameter
## 1093 posterior stabilized,curved Oval Dome Patella 3-peg 35
print(knee[1775, ])
## Surgeon Year Age Gender Weight Height BMI Diagnosis Race Side
## 1775 3 2014 22 Male 240 77 28.49 Post-trauma White Right
## KneeScore_Surgeon KneeScore_Patient GPS Manufacturer
## 1775 32 65 No Zimmer
## FemoralComponentModel FemoralComponentSize FemoralComponentType
## 1775 Persona 12 cruciate retaining
## TibialTrayModel TibialTraySize TibialInsertModel TibialInsertWidth
## 1775 Persona H Persona 10
## TibialInsertType PatellaModel PatellaDiameter
## 1775 Fixed bearing Persona 38
Each of these has a suspect factor entry. Perhaps the entry only occurs infrequently in the database and is causing the entire row to be flagged as high leverage? Try pulling the suspect columns out of the LM and see what happens.
pat_model_nine = lm(KneeScore_Patient ~ . - TibialInsertType - FemoralComponentModel - PatellaModel - TibialTrayModel - FemoralComponentType, data = knee)
evaluate(pat_model_nine)
## Test Result
## 1 Shapiro Wilk pvalue 2.75403e-14
## 2 Breusch-Pagan pvalue 0.08531339
## 3 R Squared 0.2986236
## 4 Adj R Squared 0.259491
## 5 Cross Validation 16.96213
## 6 Large Hat Values 137